Results#

Data associated with the results presented here can be found at: https://github.com/courtois-neuromod/anat-processing/releases.

Brain#

This section presents results of brain MRI data. Below are quantitative T1 values computed using the MP2RAGE and the MTsat methods. These values are averaged within the gray matter and white matter masks.

Gray matter qMRI#

Code imports#

# Python imports 
from IPython.display import clear_output
from pathlib import Path
import numpy as np
import pandas as pd

# Import custom tools
from tools.data import Data
from tools.plot import Plot

Download data#

data_type = 'brain'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Load data and plot it#

dataset.load()
fig_gm = Plot(dataset, plot_name = 'new-fig-2')

fig_gm.title = 'Brain gray matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_gm.display('jupyter-book', tissue = 'GM')
     subject  session acquisition  metric       unit label      mean  \
0          1        1     MP2RAGE   T1map     second    GM   1.48850   
1          1        1     MP2RAGE   T1map     second    WM   0.94136   
2          1        2     MP2RAGE   T1map     second    GM   1.46510   
3          1        2     MP2RAGE   T1map     second    WM   0.94620   
4          1        3     MP2RAGE   T1map     second    GM   1.28500   
..       ...      ...         ...     ...        ...   ...       ...   
123        6        4         NaN  MTRmap    percent    WM  53.09780   
124        6        4         MTS   MTsat  arbitrary    GM   8.51250   
125        6        4         MTS   MTsat  arbitrary    WM   8.55280   
126        6        4         MTS   T1map     second    GM   1.53840   
127        6        4         MTS   T1map     second    WM   1.01220   

           std    median      iqr  ...        q3  \
0      0.15877   1.48480  0.18402  ...   1.58070   
1      0.17416   0.87470  0.11626  ...   0.95667   
2      0.17762   1.47210  0.18738  ...   1.56700   
3      0.18076   0.87387  0.12917  ...   0.96739   
4      0.41732   1.41230  0.59626  ...   1.62630   
..         ...       ...      ...  ...       ...   
123    6.36400  54.32840  4.36430  ...  56.20390   
124  199.60140   1.72020  0.88756  ...   2.24390   
125  235.75970   4.07040  1.01800  ...   4.46410   
126    2.03670   1.73570  1.29400  ...   2.10790   
127    0.41837   1.03040  0.41547  ...   1.25520   

                                                   map  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
..                                                 ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...   

                                                  mask        software  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
..                                                 ...             ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   

                    date                                        map_basedon  \
0    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
1    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
2    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
3    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
4    2021-07-24 21:42:37                        sub-01_ses-003_UNIT1.nii.gz   
..                   ...                                                ...   
123  2021-07-24 22:57:39  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
124  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
125  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
126  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
127  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   

          runtime                   OS  \
0    Octave 5.2.0  x86_64-pc-linux-gnu   
1    Octave 5.2.0  x86_64-pc-linux-gnu   
2    Octave 5.2.0  x86_64-pc-linux-gnu   
3    Octave 5.2.0  x86_64-pc-linux-gnu   
4    Octave 5.2.0  x86_64-pc-linux-gnu   
..            ...                  ...   
123  Octave 5.2.0  x86_64-pc-linux-gnu   
124  Octave 5.2.0  x86_64-pc-linux-gnu   
125  Octave 5.2.0  x86_64-pc-linux-gnu   
126  Octave 5.2.0  x86_64-pc-linux-gnu   
127  Octave 5.2.0  x86_64-pc-linux-gnu   

                                        map_reference   data_type  
0    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
1    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
2    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
3    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
4    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
..                                                ...         ...  
123                                               NaN  derivative  
124                 https://doi.org/10.1002/mrm.21732  derivative  
125                 https://doi.org/10.1002/mrm.21732  derivative  
126                 https://doi.org/10.1002/mrm.21732  derivative  
127                 https://doi.org/10.1002/mrm.21732  derivative  

[128 rows x 23 columns]

White matter qMRI#

fig_wm = Plot(dataset, plot_name = 'new-fig-4')

fig_wm.title = 'Brain white matter qMRI microstructure'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_wm.display('jupyter-book', tissue = 'WM')
     subject  session acquisition  metric       unit label      mean  \
0          1        1     MP2RAGE   T1map     second    GM   1.48850   
1          1        1     MP2RAGE   T1map     second    WM   0.94136   
2          1        2     MP2RAGE   T1map     second    GM   1.46510   
3          1        2     MP2RAGE   T1map     second    WM   0.94620   
4          1        3     MP2RAGE   T1map     second    GM   1.28500   
..       ...      ...         ...     ...        ...   ...       ...   
123        6        4         NaN  MTRmap    percent    WM  53.09780   
124        6        4         MTS   MTsat  arbitrary    GM   8.51250   
125        6        4         MTS   MTsat  arbitrary    WM   8.55280   
126        6        4         MTS   T1map     second    GM   1.53840   
127        6        4         MTS   T1map     second    WM   1.01220   

           std    median      iqr  ...        q3  \
0      0.15877   1.48480  0.18402  ...   1.58070   
1      0.17416   0.87470  0.11626  ...   0.95667   
2      0.17762   1.47210  0.18738  ...   1.56700   
3      0.18076   0.87387  0.12917  ...   0.96739   
4      0.41732   1.41230  0.59626  ...   1.62630   
..         ...       ...      ...  ...       ...   
123    6.36400  54.32840  4.36430  ...  56.20390   
124  199.60140   1.72020  0.88756  ...   2.24390   
125  235.75970   4.07040  1.01800  ...   4.46410   
126    2.03670   1.73570  1.29400  ...   2.10790   
127    0.41837   1.03040  0.41547  ...   1.25520   

                                                   map  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...   
..                                                 ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...   

                                                  mask        software  \
0    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
1    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
2    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
3    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
4    /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
..                                                 ...             ...   
123  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
124  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
125  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
126  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   
127  /Users/agah/Desktop/KuzuData/anat/derivatives/...  qMRLab 2  5  0   

                    date                                        map_basedon  \
0    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
1    2021-07-24 21:40:04                        sub-01_ses-001_UNIT1.nii.gz   
2    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
3    2021-07-24 21:40:05                        sub-01_ses-002_UNIT1.nii.gz   
4    2021-07-24 21:42:37                        sub-01_ses-003_UNIT1.nii.gz   
..                   ...                                                ...   
123  2021-07-24 22:57:39  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
124  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
125  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
126  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   
127  2021-07-24 23:19:58  sub-06_ses-004_acq-MTon_MTS_aligned.nii.gz|sub...   

          runtime                   OS  \
0    Octave 5.2.0  x86_64-pc-linux-gnu   
1    Octave 5.2.0  x86_64-pc-linux-gnu   
2    Octave 5.2.0  x86_64-pc-linux-gnu   
3    Octave 5.2.0  x86_64-pc-linux-gnu   
4    Octave 5.2.0  x86_64-pc-linux-gnu   
..            ...                  ...   
123  Octave 5.2.0  x86_64-pc-linux-gnu   
124  Octave 5.2.0  x86_64-pc-linux-gnu   
125  Octave 5.2.0  x86_64-pc-linux-gnu   
126  Octave 5.2.0  x86_64-pc-linux-gnu   
127  Octave 5.2.0  x86_64-pc-linux-gnu   

                                        map_reference   data_type  
0    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
1    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
2    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
3    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
4    https://doi.org/10.1016/j.neuroimage.2009.10.002  derivative  
..                                                ...         ...  
123                                               NaN  derivative  
124                 https://doi.org/10.1002/mrm.21732  derivative  
125                 https://doi.org/10.1002/mrm.21732  derivative  
126                 https://doi.org/10.1002/mrm.21732  derivative  
127                 https://doi.org/10.1002/mrm.21732  derivative  

[128 rows x 23 columns]

Spinal cord#

Spinal cord cross-sectional area#

Download data#

data_type = 'spine'
release_version = 'latest'

dataset = Data(data_type)
dataset.download(release_version)

Load data plot it#

dataset.load()

fig_spine = Plot(dataset, plot_name = 'new-fig')

fig_spine.title = 'Spinal cord CSA [T<sub>1</sub>w/T<sub>2</sub>w]'
# If you're running this notebook in a Jupyter Notebook (eg, on MyBinder), change 'jupyter-book' to 'notebook'
fig_spine.display('jupyter-book', tissue = 'WM')
{'T1w':    Subject Session            Timestamp  \
1        1       1  2021-06-09 23:24:10   
6        1       2  2021-06-09 23:24:19   
0        1       3  2021-06-09 23:24:08   
8        2       1  2021-06-09 23:41:15   
10       2       2  2021-06-09 23:41:24   
15       2       3  2021-06-09 23:50:43   
12       2       4  2021-06-09 23:41:39   
9        3       1  2021-06-09 23:41:20   
13       3       2  2021-06-09 23:41:42   
11       3       3  2021-06-09 23:41:39   
16       3       4  2021-06-09 23:55:17   
17       4       2  2021-06-09 23:55:38   
18       4       3  2021-06-09 23:55:53   
4        5       1  2021-06-09 23:24:18   
14       5       2  2021-06-09 23:41:45   
2        6       1  2021-06-09 23:24:11   
7        6       2  2021-06-09 23:24:21   
5        6       3  2021-06-09 23:24:19   
3        6       4  2021-06-09 23:24:12   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...        31:75       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...        47:86       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...        51:93       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...         1:38       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...        12:50       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...         3:39       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...         9:46       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...        51:85       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...        33:66       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...        43:77       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...        40:74       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...        49:84       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...        43:77       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...        19:57       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...        44:82       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...        45:81       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...       89:125       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...        38:75       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...        58:95       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    67.680431   1.598728       -4.254822  ...          0.225578   
6    67.511930   1.726861       -6.577358  ...          0.186145   
0    64.109061   3.127582       -4.670983  ...          0.464761   
8    66.455289   4.204379        0.095829  ...          0.684070   
10   73.688109   2.833139       -0.068322  ...          0.406465   
15   73.905494   2.073274       -0.691532  ...          0.368828   
12   69.405673   4.568637       -0.749008  ...          0.543059   
9    59.927681   1.980624       -0.778617  ...          0.334499   
13   60.228814   1.776652       -1.464265  ...          0.247391   
11   60.621684   1.733616       -0.009478  ...          0.358365   
16   59.915665   2.030933       -2.222570  ...          0.296578   
17   59.717857   2.220913        2.572138  ...          0.399145   
18   61.969221   2.026699        6.989458  ...          0.326731   
4    53.010013  11.097434       -1.790824  ...          1.087683   
14   64.717972   4.153035       -3.034680  ...          0.567947   
2    62.953114   1.769023       -0.646246  ...          0.216321   
7    64.823566  18.835219       13.113466  ...          1.159209   
5    62.990802   2.049191       -2.338349  ...          0.298265   
3    63.925810   2.765595       -1.132526  ...          0.248317   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           10.843164          0.307774            0.680936   
6           10.874612          0.275935            0.690540   
0           10.640776          0.333651            0.690605   
8           11.992443          0.585042            0.794791   
10          12.065046          0.492764            0.756302   
15          12.371408          0.639116            0.780126   
12          12.227376          0.665839            0.796428   
9           10.086060          0.232852            0.658816   
13          10.486967          0.214164            0.716856   
11          10.632869          0.308162            0.726909   
16          10.445562          0.243935            0.716104   
17          10.999128          0.354854            0.775108   
18          10.956739          0.419218            0.753243   
4           10.965275          0.675722            0.822167   
14          11.448594          0.408139            0.769825   
2           11.513113          0.470660            0.792890   
7            9.503113          2.506067            0.576338   
5           11.506661          0.596266            0.792194   
3           11.727604          0.490648            0.803257   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.039585           2.149545          1.734302        0.980308   
6            0.031751           2.855729          1.967201        0.977647   
0            0.054994           3.202127          2.184708        0.976971   
8            0.061804           2.234122          1.464966        0.963074   
10           0.053939           2.367144          1.803792        0.966030   
15           0.052688           1.694898          1.187327        0.963111   
12           0.053488           2.145301          1.623586        0.958420   
9            0.049798           2.475063          1.644264        0.972640   
13           0.033921           1.850661          1.538691        0.966100   
11           0.049649           1.681134          1.217510        0.970807   
16           0.038919           2.551453          2.010580        0.972863   
17           0.045832           2.195005          1.555832        0.972639   
18           0.040568           2.095929          1.251544        0.976777   
4            0.059414           4.036279          2.295310        0.952220   
14           0.056204           4.103625          1.847953        0.966696   
2            0.029588           1.260913          1.049494        0.965233   
7            0.152557          22.042768         32.322329        0.968538   
5            0.041279           1.614134          1.158783        0.973527   
3            0.028672           1.754369          1.049329        0.971605   

    STD(solidity)  SUM(length)  
1        0.009615    36.167347  
6        0.008612    32.528253  
0        0.007494    34.565242  
8        0.016533    31.424022  
10       0.009791    32.356730  
15       0.014391    30.534960  
12       0.020529    31.442066  
9        0.009458    28.297791  
13       0.007298    27.236579  
11       0.010769    28.389363  
16       0.010084    28.329492  
17       0.015228    29.056988  
18       0.009427    28.313078  
4        0.027352    33.355815  
14       0.012619    32.529064  
2        0.014776    30.644730  
7        0.032237    10.122137  
5        0.010495    31.364216  
3        0.012450    31.247426  

[19 rows x 24 columns], 'T2w':    Subject Session            Timestamp  \
1        1       1  2021-06-09 23:20:54   
4        1       2  2021-06-09 23:21:02   
0        1       3  2021-06-09 23:20:52   
8        2       1  2021-06-09 23:38:23   
10       2       2  2021-06-09 23:38:28   
15       2       3  2021-06-09 23:48:42   
12       2       4  2021-06-09 23:38:42   
9        3       1  2021-06-09 23:38:25   
13       3       2  2021-06-09 23:38:46   
11       3       3  2021-06-09 23:38:40   
16       3       4  2021-06-09 23:53:25   
17       4       2  2021-06-09 23:53:48   
18       4       3  2021-06-09 23:54:02   
5        5       1  2021-06-09 23:21:05   
14       5       2  2021-06-09 23:38:47   
2        6       1  2021-06-09 23:20:55   
7        6       2  2021-06-09 23:21:12   
6        6       3  2021-06-09 23:21:05   
3        6       4  2021-06-09 23:21:00   

                                          SCT Version  \
1   git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
0   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
18  git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
1   /Users/julien/temp/neuromod/data_processed/sub...      160:201       2:3   
4   /Users/julien/temp/neuromod/data_processed/sub...      162:203       2:3   
0   /Users/julien/temp/neuromod/data_processed/sub...      161:203       2:3   
8   /Users/julien/temp/neuromod/data_processed/sub...      157:193       2:3   
10  /Users/julien/temp/neuromod/data_processed/sub...      156:191       2:3   
15  /Users/julien/temp/neuromod/data_processed/sub...      159:193       2:3   
12  /Users/julien/temp/neuromod/data_processed/sub...      160:193       2:3   
9   /Users/julien/temp/neuromod/data_processed/sub...      141:177       2:3   
13  /Users/julien/temp/neuromod/data_processed/sub...      162:198       2:3   
11  /Users/julien/temp/neuromod/data_processed/sub...      161:196       2:3   
16  /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
17  /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
18  /Users/julien/temp/neuromod/data_processed/sub...      164:199       2:3   
5   /Users/julien/temp/neuromod/data_processed/sub...      159:196       2:3   
14  /Users/julien/temp/neuromod/data_processed/sub...      154:191       2:3   
2   /Users/julien/temp/neuromod/data_processed/sub...      158:194       2:3   
7   /Users/julien/temp/neuromod/data_processed/sub...      164:200       2:3   
6   /Users/julien/temp/neuromod/data_processed/sub...      166:201       2:3   
3   /Users/julien/temp/neuromod/data_processed/sub...      167:203       2:3   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
1    80.312877   1.602798       -3.958454  ...          0.148831   
4    80.768423   1.967870       -5.074403  ...          0.180384   
0    80.774162   3.246713       -3.760068  ...          0.174290   
8    92.724125   7.198446       -0.533592  ...          0.500942   
10   94.587712   7.628431       -0.855157  ...          0.571808   
15   92.666900   8.162162       -0.596256  ...          0.609800   
12   93.571468   6.715923       -1.310382  ...          0.499746   
9    73.617773   1.283275       -0.176559  ...          0.162039   
13   72.980170   1.733563       -0.169089  ...          0.218192   
11   70.593648   1.455799       -0.991364  ...          0.267249   
16   71.268228   1.688296        0.149827  ...          0.272076   
17   74.732375   0.995570       -0.057076  ...          0.173023   
18   75.005645   0.909686        4.142686  ...          0.251494   
5    70.779953   4.773098       -1.899860  ...          0.773255   
14   74.857807   2.759146       -2.745917  ...          0.388765   
2    72.958267   2.394267       -0.230000  ...          0.206093   
7    73.129881   1.990473       -0.959923  ...          0.223915   
6    73.894805   2.227882        0.547178  ...          0.174199   
3    72.129244   2.513562       -2.145414  ...          0.180008   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
1           11.899994          0.348936            0.689786   
4           11.935064          0.352203            0.692630   
0           11.942165          0.386189            0.692055   
8           13.469831          0.903365            0.749762   
10          13.618790          0.856929            0.751709   
15          13.567128          0.933170            0.758917   
12          13.510144          0.754180            0.750687   
9           11.618506          0.249626            0.719638   
13          11.669006          0.227977            0.728585   
11          11.246244          0.328627            0.702012   
16          11.275181          0.260300            0.698106   
17          12.063074          0.345358            0.754853   
18          11.967497          0.381923            0.743363   
5           12.190368          0.565430            0.779750   
14          12.401970          0.406430            0.775455   
2           12.298752          0.455764            0.786437   
7           12.384761          0.445033            0.792261   
6           12.449794          0.470167            0.792112   
3           12.327045          0.417297            0.794967   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
1            0.032309           3.342223          1.895299        0.973535   
4            0.031759           2.725679          1.980338        0.974296   
0            0.028034           4.826952          2.124976        0.973148   
8            0.061652           3.007144          1.340842        0.970252   
10           0.060540           2.065212          1.229055        0.970512   
15           0.066758           1.366771          1.115320        0.969417   
12           0.055164           1.432686          1.105488        0.970806   
9            0.026723           1.350991          0.866047        0.970433   
13           0.027002           1.021736          0.860224        0.971586   
11           0.046127           1.260142          1.145153        0.970805   
16           0.041606           1.752418          1.216747        0.975077   
17           0.027804           2.550164          1.247343        0.967420   
18           0.040588           1.571435          1.604254        0.972454   
5            0.071128           3.074997          1.954591        0.956469   
14           0.041603           2.156050          1.223840        0.966862   
2            0.025628           0.972269          0.813403        0.972373   
7            0.026887           1.640786          1.149530        0.970194   
6            0.023507           1.604021          1.084022        0.967781   
3            0.019853           1.783156          0.920410        0.969491   

    STD(solidity)  SUM(length)  
1        0.009511    33.716889  
4        0.007769    33.951292  
0        0.006615    34.526392  
8        0.010245    31.142010  
10       0.010239    30.640014  
15       0.010025    29.350071  
12       0.009661    28.757132  
9        0.008960    29.966024  
13       0.007557    29.619905  
11       0.008657    29.249095  
16       0.009043    30.022830  
17       0.011174    29.705806  
18       0.008886    28.928858  
5        0.019386    31.359579  
14       0.013124    31.380837  
2        0.010028    30.494727  
7        0.011049    30.874411  
6        0.010371    29.962644  
3        0.009872    30.558270  

[19 rows x 24 columns], 'GMT2w':    Subject Session            Timestamp  \
0        1       1  2021-06-09 23:27:57   
5        1       2  2021-06-09 23:28:30   
1        1       3  2021-06-09 23:28:01   
8        2       1  2021-06-09 23:44:35   
9        2       2  2021-06-09 23:45:01   
14       2       3  2021-06-09 23:53:03   
11       2       4  2021-06-09 23:45:18   
10       3       1  2021-06-09 23:45:12   
13       3       2  2021-06-09 23:45:45   
12       3       3  2021-06-09 23:45:36   
15       3       4  2021-06-09 23:57:39   
16       4       2  2021-06-09 23:58:05   
17       4       3  2021-06-09 23:58:21   
4        5       1  2021-06-09 23:28:25   
2        6       1  2021-06-09 23:28:13   
7        6       2  2021-06-09 23:28:34   
6        6       3  2021-06-09 23:28:31   
3        6       4  2021-06-09 23:28:22   

                                          SCT Version  \
0   git-jca/3413-run-batch-session-c41958db922273a...   
5   git-jca/3413-run-batch-session-c41958db922273a...   
1   git-jca/3413-run-batch-session-c41958db922273a...   
8   git-jca/3413-run-batch-session-c41958db922273a...   
9   git-jca/3413-run-batch-session-c41958db922273a...   
14  git-jca/3413-run-batch-session-c41958db922273a...   
11  git-jca/3413-run-batch-session-c41958db922273a...   
10  git-jca/3413-run-batch-session-c41958db922273a...   
13  git-jca/3413-run-batch-session-c41958db922273a...   
12  git-jca/3413-run-batch-session-c41958db922273a...   
15  git-jca/3413-run-batch-session-c41958db922273a...   
16  git-jca/3413-run-batch-session-c41958db922273a...   
17  git-jca/3413-run-batch-session-c41958db922273a...   
4   git-jca/3413-run-batch-session-c41958db922273a...   
2   git-jca/3413-run-batch-session-c41958db922273a...   
7   git-jca/3413-run-batch-session-c41958db922273a...   
6   git-jca/3413-run-batch-session-c41958db922273a...   
3   git-jca/3413-run-batch-session-c41958db922273a...   

                                             Filename Slice (I->S) VertLevel  \
0   /Users/julien/temp/neuromod/data_processed/sub...          2:9       3:4   
5   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
1   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
8   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
9   /Users/julien/temp/neuromod/data_processed/sub...          3:9       3:4   
14  /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
11  /Users/julien/temp/neuromod/data_processed/sub...          3:9       3:4   
10  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
13  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
12  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
15  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
16  /Users/julien/temp/neuromod/data_processed/sub...          4:9       3:4   
17  /Users/julien/temp/neuromod/data_processed/sub...         5:10       3:4   
4   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
2   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
7   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
6   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   
3   /Users/julien/temp/neuromod/data_processed/sub...         4:10       3:4   

    MEAN(area)  STD(area)  MEAN(angle_AP)  ...  STD(diameter_AP)  \
0    15.781250   1.371800             0.0  ...          0.283857   
5    15.928571   2.034147             0.0  ...          0.312646   
1    17.000000   1.752549             0.0  ...          0.437912   
8    19.821429   1.360897             0.0  ...          0.417456   
9    20.000000   1.077365             0.0  ...          0.342271   
14   19.214286   1.605952             0.0  ...          0.487494   
11   20.464286   1.397885             0.0  ...          0.322935   
10   18.208333   1.933351             0.0  ...          0.218711   
13   17.333333   1.624466             0.0  ...          0.157746   
12   16.625000   2.452677             0.0  ...          0.185884   
15   16.958333   1.758412             0.0  ...          0.238859   
16   17.041667   1.417279             0.0  ...          0.193646   
17   17.333332   1.455354             0.0  ...          0.309761   
4    16.214286   1.848883             0.0  ...          0.490131   
2    16.642857   3.600241             0.0  ...          0.556421   
7    17.392857   2.182958             0.0  ...          0.433186   
6    16.321428   2.020936             0.0  ...          0.451914   
3    16.535714   2.707228             0.0  ...          0.719459   

    MEAN(diameter_RL)  STD(diameter_RL)  MEAN(eccentricity)  \
0            9.157261          0.632701            0.760794   
5            8.912826          0.518961            0.755229   
1            9.105736          0.577677            0.742294   
8           11.544729          0.413976            0.882456   
9           11.842302          0.579720            0.879404   
14          11.589557          0.509289            0.880191   
11          11.748837          0.339294            0.880092   
10           9.713868          0.912814            0.809431   
13           9.552361          0.850671            0.803472   
12           9.541168          0.905707            0.803929   
15           9.512255          0.787789            0.809049   
16           9.258316          0.625445            0.800148   
17           9.310330          0.966440            0.792127   
4            9.916864          0.663039            0.848935   
2           10.865812          0.972017            0.875254   
7           11.029238          0.908874            0.877292   
6           10.450533          0.889613            0.879650   
3           10.447901          0.631897            0.896789   

    STD(eccentricity)  MEAN(orientation)  STD(orientation)  MEAN(solidity)  \
0            0.065413           9.239814          4.915181        0.398420   
5            0.050143           7.501914          6.651370        0.402462   
1            0.076859           8.999431          5.426012        0.412780   
8            0.015014           2.491855          1.419888        0.400532   
9            0.021123           2.516891          2.068491        0.380244   
14           0.021772           3.755927          2.144876        0.392944   
11           0.017030           1.848681          1.410178        0.390731   
10           0.046939           2.111163          1.302024        0.441700   
13           0.048638           3.743699          2.736344        0.431054   
12           0.050888           3.033851          3.309783        0.423130   
15           0.050811           2.475007          0.736044        0.427416   
16           0.040699           3.309946          1.876603        0.438293   
17           0.067271           5.133278          3.005962        0.452724   
4            0.047865           3.056269          2.330227        0.420649   
2            0.043939           1.272704          0.738812        0.392086   
7            0.037499           1.582275          1.103783        0.406786   
6            0.036167           1.582814          1.583200        0.423449   
3            0.037479           3.565542          1.894078        0.461639   

    STD(solidity)  SUM(length)  
0        0.017171    40.000000  
5        0.017327    34.999983  
1        0.019752    35.000010  
8        0.022981    35.000033  
9        0.013678    34.999980  
14       0.018671    35.000000  
11       0.011656    35.000033  
10       0.014227    29.999989  
13       0.016436    30.000037  
12       0.022843    29.999986  
15       0.020870    29.999991  
16       0.010648    30.000011  
17       0.024747    30.000011  
4        0.020092    34.999977  
2        0.054614    34.999983  
7        0.024975    34.999990  
6        0.020716    35.000017  
3        0.037115    35.000003  

[18 rows x 24 columns]}

Gray matter cross-sectional area#

White matter qMRI#